LIU Yantong, LI Ting, JIANG Zhishu, ZENG Chuihai, HE Rong, QIU Jiao, LIN Xiaoli, PENG Limei, SONG Yongping, ZHOU Dahu, CAI Yicong, ZHU Changlan, FU Junru, HE Haohua, XU Jie

Rice Science;  2022, 29(6): 522‒534

Abstract: Semi-dwarfing improves the lodging resistance and yield of rice, and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height, resulting in reduced genetic diversity and negative agronomic traits. Thus, exploring alternative sources of dwarfism is imperative for rice breeding. Here, we identified a novel RGA1 allele, d1-w, from a local indica variety Xiaolixiang (XLX) using a map-based cloning approach. Compared with other rice varieties, RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level. The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding. Compared with transgenic XLX plants (XLXD1), XLX exhibited reduced plant height, increased stem strength, lower reactive oxygen species accumulation, delayed senescence, stronger photosynthesis, higher grain yield and quality (including external, milling and nutritional qualities), and enhanced resistance to drought and Rhizoctonia solani. Therefore, we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

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Fig. 2. Map-based cloning of DEP-SRSgene.

A, Fine mapping of DEP-SRS gene. The gene was mapped to the interval between molecular markers RM18410 and RM18448 on chromosome (Chr.) 5 and further delimited to a 125-kb genomic region between markers M4 and M5 containing 14 open reading fragments (ORFs). Numbers below the markers indicate the number of recombinants.

B, The first intron sequences of XLX and NPB. Black boxes indicate exons, black lines indicate introns, white box with arrow indicates promoter, and white box without arrow indicate 3′-UTR. Letters with yellow background indicate exon sequences, while those with red background indicate a stop code in the new transcript. Red letter with underline indicates the divergent sequence and black letter with underline indicates the splice site.

C, The divergence (A to G) in the first intron produced a new splice site in XLX. Red star indicates the SNP, and red arrow indicates a stop code in the new transcript.

D, Relative expression levels of functional RGA1/D1 transcripts. The two-week-old seedlings of XLX, NPB and TN1 were collected for qRT-PCR, and theOsACTgene was used as a control. Mean and SD values were obtained from three biological replicates. **, P < 0.01 (the Student’s t-test).

XLX, Xiaolixiang; NPB, Nipponbare; TN1, Taichung Native 1; SNP, Single nucleotide polymorphism.